[2024-01-25 19:05:20,917] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:20,919] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:20,919] [INFO] DQC Reference Directory: /var/lib/cwl/stg580ef4b7-d32c-4d04-903c-6f87c48b2222/dqc_reference
[2024-01-25 19:05:22,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:22,081] [INFO] Task started: Prodigal
[2024-01-25 19:05:22,082] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf761597-9baa-44ac-a8c0-629eb33ef86c/GCF_014637265.1_ASM1463726v1_genomic.fna.gz | prodigal -d GCF_014637265.1_ASM1463726v1_genomic.fna/cds.fna -a GCF_014637265.1_ASM1463726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:35,321] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:35,321] [INFO] Task started: HMMsearch
[2024-01-25 19:05:35,321] [INFO] Running command: hmmsearch --tblout GCF_014637265.1_ASM1463726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg580ef4b7-d32c-4d04-903c-6f87c48b2222/dqc_reference/reference_markers.hmm GCF_014637265.1_ASM1463726v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:35,606] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:35,607] [INFO] Found 6/6 markers.
[2024-01-25 19:05:35,648] [INFO] Query marker FASTA was written to GCF_014637265.1_ASM1463726v1_genomic.fna/markers.fasta
[2024-01-25 19:05:35,648] [INFO] Task started: Blastn
[2024-01-25 19:05:35,649] [INFO] Running command: blastn -query GCF_014637265.1_ASM1463726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg580ef4b7-d32c-4d04-903c-6f87c48b2222/dqc_reference/reference_markers.fasta -out GCF_014637265.1_ASM1463726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:36,505] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:36,510] [INFO] Selected 14 target genomes.
[2024-01-25 19:05:36,510] [INFO] Target genome list was writen to GCF_014637265.1_ASM1463726v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:36,519] [INFO] Task started: fastANI
[2024-01-25 19:05:36,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf761597-9baa-44ac-a8c0-629eb33ef86c/GCF_014637265.1_ASM1463726v1_genomic.fna.gz --refList GCF_014637265.1_ASM1463726v1_genomic.fna/target_genomes.txt --output GCF_014637265.1_ASM1463726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:52,281] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:52,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg580ef4b7-d32c-4d04-903c-6f87c48b2222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:52,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg580ef4b7-d32c-4d04-903c-6f87c48b2222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:52,292] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:05:52,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:52,292] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	100.0	1656	1658	95	conclusive
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	99.9948	1656	1658	95	conclusive
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	84.4453	1098	1658	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	84.3457	1095	1658	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	82.3654	875	1658	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	81.8102	885	1658	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	80.3402	677	1658	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	80.1866	783	1658	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	80.0666	750	1658	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	79.6335	623	1658	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	79.5914	672	1658	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.5195	505	1658	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1853	458	1658	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.8376	385	1658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:52,293] [INFO] DFAST Taxonomy check result was written to GCF_014637265.1_ASM1463726v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:52,294] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:52,294] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:52,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg580ef4b7-d32c-4d04-903c-6f87c48b2222/dqc_reference/checkm_data
[2024-01-25 19:05:52,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:52,343] [INFO] Task started: CheckM
[2024-01-25 19:05:52,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014637265.1_ASM1463726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014637265.1_ASM1463726v1_genomic.fna/checkm_input GCF_014637265.1_ASM1463726v1_genomic.fna/checkm_result
[2024-01-25 19:06:39,257] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:39,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:39,277] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:39,277] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:39,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014637265.1_ASM1463726v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:39,278] [INFO] Task started: Blastn
[2024-01-25 19:06:39,279] [INFO] Running command: blastn -query GCF_014637265.1_ASM1463726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg580ef4b7-d32c-4d04-903c-6f87c48b2222/dqc_reference/reference_markers_gtdb.fasta -out GCF_014637265.1_ASM1463726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:40,825] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:40,828] [INFO] Selected 8 target genomes.
[2024-01-25 19:06:40,828] [INFO] Target genome list was writen to GCF_014637265.1_ASM1463726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:40,835] [INFO] Task started: fastANI
[2024-01-25 19:06:40,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf761597-9baa-44ac-a8c0-629eb33ef86c/GCF_014637265.1_ASM1463726v1_genomic.fna.gz --refList GCF_014637265.1_ASM1463726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014637265.1_ASM1463726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:51,063] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:51,070] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:51,070] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_001969385.1	s__Salipiger profundus	99.9948	1656	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	conclusive
GCF_000153725.1	s__Salipiger bermudensis	84.4254	1101	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_900102075.1	s__Salipiger thiooxidans	84.3368	1096	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_017311415.1	s__Salipiger abyssi_A	83.5985	981	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	83.382	988	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	82.9394	943	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223355.1	s__Salipiger pacificus_B	81.8901	905	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109705.1	s__Roseivivax marinus	80.3402	677	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:51,072] [INFO] GTDB search result was written to GCF_014637265.1_ASM1463726v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:51,072] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:51,075] [INFO] DFAST_QC result json was written to GCF_014637265.1_ASM1463726v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:51,075] [INFO] DFAST_QC completed!
[2024-01-25 19:06:51,075] [INFO] Total running time: 0h1m30s